Man pages for AdrijaK/omicsWrappers
wrapper functions for integrating and visualising ChIPseq, ATACseq, Hi-C, pcHi-C and RNAseq data
| CandidateInteractionsToGInteractions | CandidateInteractionsToGInteractions transform Chicdiff... |
| chicDiffToGI | chicDiffToGI converts ChicDiff resultsMatrix to a... |
| countChIPPeaksInPromoters | countChIPPeaksInPromoters count ChIP peaks in promoters of... |
| countFeatureSet | countFeatureSet counts overlaps between 'GRangesObject' and... |
| countReadsInGranges | countReadsInGranges counts reads in aligned BAM files for... |
| findGOTerms | findGOTerms Find a list of GO terms based on keywords based... |
| findMouseGenesFromGO | findMouseGenesFromGO find mouse genes based on one or many GO... |
| loadBed6AsGRanges | load snakePipes DiffBinding_allregions.bed BED6 file as... |
| loadFilteredResultsAsGRanges | load snakePipes Filtered.results.*.bed file as GRanges object... |
| makeFeaturesList | create a features list from snakePipes ChIP pipeline |
| plotFeatureOverlaps | plot the overlaps with features in a particular way |
| plotOverlapsWithFeaturesList | a wrapper function that plots promoter (GRanges) overlaps... |
| removeAllAfterDot | removeAllAfterDot a convenience function for extracting gene... |
| summarizeOverlapsWithFeatureList | Summarize overlaps with a feature list |
| writeGRanges2BED | write GRanges object to BED6 format, converting 1-based... |
